We analyzed mitochondrial DNA variation in honey bee colonies in Jordan using DraI restriction profiles of the COI-COII intergenic region. Seven different haplotypes were observed, three of which belonged to the C mitochondrial lineage. Samples displaying haplotypes of the C lineage were concentrated in the north of the country where frequent importations of European bees have occurred. We conclude that the C mitochondrial haplotypes found in the study reflect past or recent importations of non-native honey bees. No C haplotypes were detected in areas that have been identified as possible source populations for the conservation of original A. m. syriaca in the south of the sampling region, thus confirming the existence of comparatively pure genetic resources of this subspecies in Jordan.

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